(Havent read the whole thread but~)
a lot of this seems based around "organic ships" and the like. Like gigamishu, etc. (also super scary giant mishu art there, wesman!)
I think if there are actual creatures in space tho, And ignoring the reasons they cant exist (like microscopic dust cutting through them like a bullet or intense heat or radiation or cold killing them) what kind of creatures might we have?
If we stick with the elements of the setting at hand i thing it should revolve around Aether somehow. Being that kind of just pass through our detention and are either crystalline beings that are based off energy and not basic electrical impulse or aetheric beings (i don't mean they damage you with aether i mean they are from the same place aether is from and like aether they bleed into our realm).
Like little crystal bugs on a ships hull that can grow and cause infestations. Or creates that kind of bleed through when a lot of aether is thrown around (like when fleets of ships are present, Or while fighting with aether weapons.)
This also means installations with aether, or entropy causing power sources like nep, yamatai, and origin might kind of effect their ecosystems as more and more transdimensional beings kind of pop up near their facilities, stations, ships, etc. I don't know much about the NDC but I'm sure we can involve them in that too as just our FTL and power systems effect our surroundings more than just aether ships arent healthy to use in a planets atmosphere
Also the idea of crystal based infestations on planets is a nice RP idea when some Aether thing or large scale powersource goes critical and you gotta deploy the NSMC, Star Army, Dusk liegon, etc. just to clean it up because they are siphoning power from the bleed out and spreading like kudzu and people are power in a sense so they arent ignored by these creatures or growths...